Research workbench
Thdp-MN2+ complex of R413A variant of ecmend soaked with 2- ketoglutarate for 35 min
Analyse Thdp-MN2+ complex of R413A variant of ecmend soaked with 2- ketoglutarate for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EJM
- Type
- protein
- Length
- 4,448 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
- EC
- 2.2.1.9
- UniProt
- P17109
- Ligands
- TD5, MN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 556 | 41% helix, 16% strand | P17109 |
Ligands and binding sites
- TD5 · (4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.87 | 0.88 | 153 | TD5 |
| 2 | 594 | 0.85 | 0.90 | 95 | TD5 |
| 3 | 491 | 0.85 | 0.91 | 88 | TD5 |
| 4 | 569 | 0.85 | 0.90 | 90 | TD5 |
| 5 | 632 | 0.85 | 0.89 | 95 | TD5, MN |
Interfaces
15 interfaces between chains.
- A–B · 3505 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 3492 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3488 Ų buried · 51 hydrogen bonds · protein-protein
- G–H · 3477 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 1553 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5EJM · ThDP-Mn2+ complex of R413A variant of EcMenD soaked with 2-ketoglutarate for 35 min · the same entry in another collection · chain H against H, TM-score 1.00
- P17109 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P17109
- Elsewhere: RCSB PDB 5EJM · PDBe 5EJM · UniProt P17109
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